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- PDB-4pqo: Structure of the human SNX14 PX domain in space group I41 -

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Basic information

Entry
Database: PDB / ID: 4pqo
TitleStructure of the human SNX14 PX domain in space group I41
ComponentsSorting nexin-14
KeywordsPROTEIN TRANSPORT / sorting nexin / phox homology domain / phosphoinositide binding
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate binding / postsynaptic modulation of chemical synaptic transmission / autophagosome maturation / phosphatidylinositol binding / protein transport / late endosome / late endosome membrane / postsynapse / lysosome / lysosomal membrane ...phosphatidylinositol-3,5-bisphosphate binding / postsynaptic modulation of chemical synaptic transmission / autophagosome maturation / phosphatidylinositol binding / protein transport / late endosome / late endosome membrane / postsynapse / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / dendrite / cytosol
Similarity search - Function
Sorting nexin-14, PX domain / SNX14, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / Phox-like domain / PX Domain ...Sorting nexin-14, PX domain / SNX14, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / Regulator of G protein signaling domain / RGS, subdomain 2 / PX domain profile. / PX domain / Phox homology / RGS domain / PX domain superfamily / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMas, C. / Norwood, S. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Teasdale, R. / Collins, B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Different Phosphoinositide Specificities of the PX Domains of Sorting Nexins Regulating G-protein Signaling.
Authors: Mas, C. / Norwood, S.J. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Ghai, R. / Ona Yanez, L.E. / Davis, J.L. / Teasdale, R.D. / Collins, B.M.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-14


Theoretical massNumber of molelcules
Total (without water)15,2271
Polymers15,2271
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.840, 86.840, 74.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Sorting nexin-14 / SNX14


Mass: 15227.159 Da / Num. of mol.: 1 / Fragment: PX domain (UNP residues 561-686)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5W7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.61 Å3/Da / Density % sol: 73.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.8 M ammonium citrate tribasic, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→61.405 Å / Num. all: 9092 / Num. obs: 9067 / % possible obs: 99.8 % / Observed criterion σ(I): 1.9
Reflection shellHighest resolution: 2.55 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→22.098 Å / σ(F): 1.93 / Phase error: 23.12 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2088 432 4.76 %
Rwork0.1834 --
obs0.1882 9067 99.89 %
all-9075 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→22.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 0 23 915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01919
X-RAY DIFFRACTIONf_angle_d1.261242
X-RAY DIFFRACTIONf_dihedral_angle_d18.77342
X-RAY DIFFRACTIONf_chiral_restr0.089128
X-RAY DIFFRACTIONf_plane_restr0.006158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.92030.30261650.30512810X-RAY DIFFRACTION94
2.9203-3.67570.22741310.21222871X-RAY DIFFRACTION96
3.6757-20.26690.18551360.15182921X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7876-2.95133.9964.0211-1.63496.34080.3097-0.2469-0.1235-0.10080.20870.18270.06040.0823-0.42480.23020.03010.08960.3289-0.08160.395435.265951.600313.9911
24.095-1.3473-0.26145.29890.44594.83440.0395-0.16620.0546-0.17130.13010.39530.2015-0.3182-0.15830.19950.0204-0.0710.298-0.0250.45228.009452.279611.939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 562:630)
2X-RAY DIFFRACTION2chain 'A' and (resseq 631:686)

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